TMFoldRec: a statistical potential-based transmembrane protein fold recognition tool.

BACKGROUND: Transmembrane proteins (TMPs) are the key components of signal transduction, cell-cell adhesion and energy and material transport into and out from the cells. For the deep understanding of these processes, structure determination of transmembrane proteins is indispensable. However, due to technical difficulties, only a few transmembrane protein structures have been determined experimentally. Large-scale genomic sequencing provides increasing amounts of sequence information on the proteins and whole proteomes of living organisms resulting in the challenge of bioinformatics; how the structural information should be gained from a sequence. RESULTS: Here, we present a novel method, TMFoldRec, for fold prediction of membrane segments in transmembrane proteins. TMFoldRec based on statistical potentials was tested on a benchmark set containing 124 TMP chains from the PDBTM database. Using a 10-fold jackknife method, the native folds were correctly identified in 77 % of the cases. This accuracy overcomes the state-of-the-art methods. In addition, a key feature of TMFoldRec algorithm is the ability to estimate the reliability of the prediction and to decide with an accuracy of 70 %, whether the obtained, lowest energy structure is the native one. CONCLUSION: These results imply that the membrane embedded parts of TMPs dictate the TM structures rather than the soluble parts. Moreover, predictions with reliability scores make in this way our algorithm applicable for proteome-wide analyses. AVAILABILITY: The program is available upon request for academic use

Full Circle or Spiralling Out of Control?: State Violence and the Control of Urbanisation in Papua New Guinea

There is an administrative reluctance to recognise the permanency of urban settlement in Papua New Guinea. This reluctance, evident since the 1960s, has been characteristic of both the colonial and post-colonial administrations. Opposition to some facets of urbanisation continues today, despite growing population and land pressures in most rural areas and real problems of landlessness emerging in particular rural areas. Colonial control of urban populations has been replicated in contemporary times, often in more draconian form. Eviction of urban settlers has been tied to issues of crime and urban respectability, and lingering perceptions that Melanesians should be rural residents. The growth of informal settlements and urbanisation are not seen as issues of urban planning, nor is the context of urban migration linked to socioeconomic inequality, hence other forms of urban policy are largely absent. Strengthening alliances between land-owners and the state (especially police and provincial administrations) have thus emphasised intraurban inequality and hampered national development

Rural-to-Urban Labor Migration, Household Livelihoods, and the Rural Environment in Chongqing Municipality, Southwest China

Rural migration and its relationship to the rural environment have attracted increasing research interest in recent decades. Rural migration constitutes a key component of human population movement, while rural areas contain most of the world’s natural resources such as land and forests. This study empirically evaluates a conceptual framework incorporating rural household livelihoods as an integrative mediating factor between rural migration and the rural environment in the context of rural-to-urban labor migration in Chongqing Municipality, Southwest China. The analysis draws on data collected through household surveys and key informant interviews from four villages. Results confirm the hypothesis that labor-migrant and non-labor-migrant households differ significantly in livelihood activities including agricultural production, agricultural technology use, income and consumption, and resource use and management. Implications for the subsequent environmental outcomes of rural labor out-migration and corresponding natural resource management and policy in rural origin areas are discussed

Development of a new microstructure-based constitutive model for healthy and cancerous tissue

1 pageinfo:eu-repo/semantics/publishe

Inferring microstructural tissue properties in healthy and cancerous tissues via elasti- city imaging

1 pageinfo:eu-repo/semantics/publishe

A new microstructure-based constitutive model for healthy and cancerous tissue applied to elasticity imaging

1 pageinfo:eu-repo/semantics/publishe